Transcriptome profiling of colorectal adenocarcinoma HT-29 cells after 5-FU treatment

We performed RNA-Seq analysis of transcriptomic alterations in HT-29 colon cancer cells treated with 20 µM 5-FU for 72 h, the time period roughly equivalent to three consecutive cell doublings. We expected that the high dose of the drug, which corresponds to 10 x IC50 and kills nearly 80% of cells, would selectively favor the survival of cells that acquire a transient resistance to 5-FU.We identified lincRNAs LINC00973, LINC00941, CCAT1, and CASC19 as the most upregulated in 5-FU treated HT-29 cells. These results were further validated by RT-qPCR in HT-29 cells harvested after 72 h and 144 h of treatment with 2 µM 5-FU or 2 µM OXP (corresponding to the IC50 dose) or 5 µM IRI (one third of its IC50).We also added lincRNA BCAR4 to the analysis, which is undetectable by RNA-Seq, but according to our RT-qPCR data is upregulated in 57% of colorectal tumors. Obtained results demonstrated that all five lincRNAs are upregulated by the treatment with all three drugs, indicating that monitoring by RT-qPCR of just two of the lincRNAs (LINC00973 and BCAR4) provides a robust instrument for distinguishing of untreated and treated cells.